Ancestry-specific effects of APOE on Alzheimer Disease Endophenotypes

Importance: APOE e4 is the strongest genetic risk factor for Alzheimer's disease (AD), yet its effect varies across ancestral populations. As blood-based biomarkers increasingly inform AD diagnosis, failure to account for both APOE genotype and ancestry could lead to misinterpretation of biomarker profiles and inaccurate diagnostic classification. Understanding how ancestry modulates APOE effects is crucial for ensuring accurate biomarker-based assessments and AD diagnosis. Objective: To determine whether genetic ancestry modulates APOE association with cognitive function, brain morphometry, and plasma biomarkers. Design, Setting, Participants: Cross-sectional analysis of community-dwelling older adults from the Health and Aging Brain Study-Health Disparities (HABS-HD) cohort (N = 2733). Participants spanning the cognitive spectrum underwent cognitive assessment, neuroimaging, plasma biomarker collection, and genome-wide genotyping from 2018 to 2023. Main Outcomes and Measures: Cognitive performance (global cognition, memory, executive function, verbal ability), brain morphometry (cortical thickness, hippocampal volume), and plasma biomarkers (AB42/AB40, pTau181, pTau217, total tau, NfL). Results: In the full cohort, APOE e4+ was associated with worse cognitive performance across all domains, reduced cortical thickness and hippocampal volume, lower AB42/AB40, and elevated pTau181 and pTau217. APOE e2+ was associated with lower pTau217. Ancestry-stratified analyses revealed attenuated e4+ effects on pTau217 and pTau181 in African compared with European participants (~2.5-fold for both), with the pTau217 difference surviving FDR correction. Compositional analysis confirmed that e4+ effects on pTau181 and pTau217 strengthened with increasing European ancestry proportion. Local ancestry analysis showed e4+ effects on pTau217 were significantly attenuated in individuals with African local ancestry at the APOE locus. In contrast, e4+ effects on AB42/AB40, cognition, and neuroimaging were largely consistent across ancestry groups. Meta-analysis with an independent multi-ancestry cohort replicated the attenuated pTau181 findings. Conclusions and Relevance: Genetic ancestry modifies the effect of APOE on AD endophenotypes. In particular, African ancestry attenuates the association between APOE e4+ and pTau181 and pTau217. Accurate AD diagnosis requires consideration of both APOE genotype and ancestry to avoid misclassification in biomarker-based evaluations.